Galaxy Macromolecular Coarse-Grained Flexibility tutorial
Version 1

Workflow Type: Galaxy
Stable

Macromolecular Coarse-Grained Flexibility (FlexServ) tutorial using BioExcel Building Blocks (biobb)

This tutorial aims to illustrate the process of generating protein conformational ensembles from 3D structures and analysing its molecular flexibility, step by step, using the BioExcel Building Blocks library (biobb).


Copyright & Licensing

This software has been developed in the MMB group at the BSC & IRB for the European BioExcel, funded by the European Commission (EU H2020 823830, EU H2020 675728).

Licensed under the Apache License 2.0, see the file LICENSE for details.

Steps

ID Name Description
0 Fetch structure biobb_io_pdb_ext
1 ExtractAtoms biobb_structure_utils_extract_atoms_ext
2 NmaRun biobb_flexserv_nma_run_ext
3 DmdRun biobb_flexserv_dmd_run_ext
4 BdRun biobb_flexserv_bd_run_ext
5 CpptrajRms NMA biobb_analysis_cpptraj_rms_ext
6 PczZip NMA biobb_flexserv_pcz_zip_ext
7 CpptrajRms DMD biobb_analysis_cpptraj_rms_ext
8 PczZip DMD biobb_flexserv_pcz_zip_ext
9 CpptrajRms BD biobb_analysis_cpptraj_rms_ext
10 PczZip BD biobb_flexserv_pcz_zip_ext
11 PczUnzip NMA biobb_flexserv_pcz_unzip_ext
12 PczBfactor NMA biobb_flexserv_pcz_bfactor_ext
13 PczAnimate NMA biobb_flexserv_pcz_animate_ext
14 PczInfo NMA biobb_flexserv_pcz_info_ext
15 PczEvecs NMA biobb_flexserv_pcz_evecs_ext
16 PczStiffness NMA biobb_flexserv_pcz_stiffness_ext
17 PczCollectivity NMA biobb_flexserv_pcz_collectivity_ext
18 PczUnzip DMD biobb_flexserv_pcz_unzip_ext
19 PczUnzip BD biobb_flexserv_pcz_unzip_ext
20 PczHinges DynDon biobb_flexserv_pcz_hinges_ext
21 PczHinges Bfactor biobb_flexserv_pcz_hinges_ext
22 PczHinges FCTE biobb_flexserv_pcz_hinges_ext
23 CpptrajRms NMA 2 biobb_analysis_cpptraj_rms_ext
24 CpptrajConvert NMA biobb_analysis_cpptraj_convert_ext
25 CpptrajRms DMD 2 biobb_analysis_cpptraj_rms_ext
26 CpptrajRms BD 2 biobb_analysis_cpptraj_rms_ext

Outputs

ID Name Description Type
_anonymous_output_1 #main/_anonymous_output_1 n/a
  • File
_anonymous_output_10 #main/_anonymous_output_10 n/a
  • File
_anonymous_output_11 #main/_anonymous_output_11 n/a
  • File
_anonymous_output_12 #main/_anonymous_output_12 n/a
  • File
_anonymous_output_13 #main/_anonymous_output_13 n/a
  • File
_anonymous_output_14 #main/_anonymous_output_14 n/a
  • File
_anonymous_output_15 #main/_anonymous_output_15 n/a
  • File
_anonymous_output_16 #main/_anonymous_output_16 n/a
  • File
_anonymous_output_2 #main/_anonymous_output_2 n/a
  • File
_anonymous_output_3 #main/_anonymous_output_3 n/a
  • File
_anonymous_output_4 #main/_anonymous_output_4 n/a
  • File
_anonymous_output_5 #main/_anonymous_output_5 n/a
  • File
_anonymous_output_6 #main/_anonymous_output_6 n/a
  • File
_anonymous_output_7 #main/_anonymous_output_7 n/a
  • File
_anonymous_output_8 #main/_anonymous_output_8 n/a
  • File
_anonymous_output_9 #main/_anonymous_output_9 n/a
  • File
bd_ensemble.log #main/bd_ensemble.log n/a
  • File
bd_ensemble.mdcrd #main/bd_ensemble.mdcrd n/a
  • File
bd_ensemble.pcz #main/bd_ensemble.pcz n/a
  • File
bd_ensemble_rmsd.dat #main/bd_ensemble_rmsd.dat n/a
  • File
bd_ensemble_rmsd.dcd #main/bd_ensemble_rmsd.dcd n/a
  • File
bd_ensemble_uncompressed.crd #main/bd_ensemble_uncompressed.crd n/a
  • File
bfactor_all.dat #main/bfactor_all.dat n/a
  • File
bfactor_all.pdb #main/bfactor_all.pdb n/a
  • File
dmd_ensemble.log #main/dmd_ensemble.log n/a
  • File
dmd_ensemble.mdcrd #main/dmd_ensemble.mdcrd n/a
  • File
hinges_bfactor_report.json #main/hinges_bfactor_report.json n/a
  • File
mypdb.pdb #main/mypdb.pdb n/a
  • File
nma_ensemble.log #main/nma_ensemble.log n/a
  • File
nma_ensemble.mdcrd #main/nma_ensemble.mdcrd n/a
  • File
pcz_collectivity.json #main/pcz_collectivity.json n/a
  • File
pcz_evecs.json #main/pcz_evecs.json n/a
  • File
pcz_proj1.crd #main/pcz_proj1.crd n/a
  • File
pcz_proj1.dcd #main/pcz_proj1.dcd n/a
  • File
pcz_report.json #main/pcz_report.json n/a
  • File
pcz_stiffness.json #main/pcz_stiffness.json n/a
  • File
structure_ca.pdb #main/structure_ca.pdb n/a
  • File

Version History

Version 1 (earliest) Created 11th Aug 2023 at 09:32 by Genís Bayarri

Initial commit


Frozen Version-1 8b2c420
help Creators and Submitter
Citation
Hospital, A., & Bayarri, G. (2023). Galaxy Macromolecular Coarse-Grained Flexibility tutorial. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.557.1
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Created: 11th Aug 2023 at 09:32

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